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Escherichia coli K-12 substr. MG1655 Enzyme: endonuclease IV

Gene: nfo Accession Numbers: EG10651 (EcoCyc), b2159, ECK2152

Regulation Summary Diagram: ?

Regulation summary diagram for nfo

Damaged bases in DNA occur due to alkylating agents, ionizing radiation or oxidants such as superoxide radicals, hydrogen peroxide and hydroxyl radicals. Base excision repair (BER) works to repair damaged DNA by multiple steps: removal of the damaged base by a cleavage of the glycosidic bond by a glycosylase enzyme generating an apyyrimidinic or apurinic (AP) site; removal of the AP site by an AP endonuclease; resynthesis of the excised strand by DNA polymerase using the intact strand as template and ligation by DNA ligase. Nfo is one of two (the other being XthA) 5' AP endonucleases in Escherichia coli. Nfo has been purified and shown to catalyze the formation of single-stand breaks in double stranded AP DNA [Levin88, Cunningham86]. Nfo has been shown to function in a manner similar to Exonuclease III (XthA) in removing phosphoglycoaldehyde, phosphate, deoxyribose-5-phosphate, 4-hydroxy-2-pentenal residues and urea residues [Doetsch90]. Unlike XthA, Nfo does not have a 3' exonuclease activity.

Gene Citations: [Ariza95]

Locations: cytosol

Map Position: [2,248,862 -> 2,249,719] (48.47 centisomes, 174°)
Length: 858 bp / 285 aa

Molecular Weight of Polypeptide: 31.479 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007146 , CGSC:14161 , DIP:DIP-47966N , EchoBASE:EB0645 , EcoGene:EG10651 , EcoliWiki:b2159 , Mint:MINT-1242700 , ModBase:P0A6C1 , OU-Microarray:b2159 , PortEco:nfo , PR:PRO_000023374 , Pride:P0A6C1 , Protein Model Portal:P0A6C1 , RefSeq:NP_416664 , RegulonDB:EG10651 , SMR:P0A6C1 , String:511145.b2159 , UniProt:P0A6C1

Relationship Links: InterPro:IN-FAMILY:IPR001719 , InterPro:IN-FAMILY:IPR013022 , InterPro:IN-FAMILY:IPR018246 , Panther:IN-FAMILY:PTHR21445 , PDB:Structure:1QTW , PDB:Structure:1QUM , PDB:Structure:2NQ9 , PDB:Structure:2NQH , PDB:Structure:2NQJ , PDB:Structure:4K1G , Pfam:IN-FAMILY:PF01261 , Prosite:IN-FAMILY:PS00729 , Prosite:IN-FAMILY:PS00730 , Prosite:IN-FAMILY:PS00731 , Prosite:IN-FAMILY:PS51432 , Smart:IN-FAMILY:SM00518

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for nfo

GO Terms:

Biological Process: GO:0000726 - non-recombinational repair Inferred from experiment [Levin88]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred from experiment Inferred by computational analysis [UniProtGOA11, Levin88]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006284 - base-excision repair Inferred by computational analysis [Gaudet10]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004519 - endonuclease activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, Levin88]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01]
GO:0003906 - DNA-(apurinic or apyrimidinic site) lyase activity Inferred by computational analysis [Gaudet10]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0008081 - phosphoric diester hydrolase activity Inferred by computational analysis [Gaudet10]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06, GOA01]
GO:0008833 - deoxyribonuclease IV (phage-T4-induced) activity Inferred by computational analysis [GOA06, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection radiation
information transfer DNA related DNA degradation
metabolism degradation of macromolecules DNA

Essentiality data for nfo knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Revised 25-May-2011 by Brito D

Enzymatic reaction of: deoxyribonuclease IV (endonuclease IV)

EC Number:

a single stranded DNA + n H2O <=> n a 5'-phosphooligonucleotide

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of endonuclease IV with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 10
[Saporito88, UniProt10a]
UniProt: (in Ref. 1; AAA24216);
Metal-Binding-Site 69
UniProt: Zinc 1.
Metal-Binding-Site 109
UniProt: Zinc 1.
Metal-Binding-Site 145
UniProt: Zinc 1.
Metal-Binding-Site 179
UniProt: Zinc 2.
Metal-Binding-Site 182
UniProt: Zinc 3.
Metal-Binding-Site 216
UniProt: Zinc 2.
Metal-Binding-Site 229
UniProt: Zinc 3.
Metal-Binding-Site 231
UniProt: Zinc 3.
Metal-Binding-Site 261
UniProt: Zinc 2.
Sequence-Conflict 273
[Richterich93, UniProt15]
UniProt: (in Ref. 2; AAA60529).

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b2159 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10651; confirmed by SwissProt match.


Ariza95: Ariza RR, Li Z, Ringstad N, Demple B (1995). "Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli Rob protein." J Bacteriol 1995;177(7);1655-61. PMID: 7896685

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Cunningham86: Cunningham RP, Saporito SM, Spitzer SG, Weiss B (1986). "Endonuclease IV (nfo) mutant of Escherichia coli." J Bacteriol 168(3);1120-7. PMID: 2430946

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Doetsch90: Doetsch PW, Cunningham RP (1990). "The enzymology of apurinic/apyrimidinic endonucleases." Mutat Res 236(2-3);173-201. PMID: 1697933

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Levin88: Levin JD, Johnson AW, Demple B (1988). "Homogeneous Escherichia coli endonuclease IV. Characterization of an enzyme that recognizes oxidative damage in DNA." J Biol Chem 263(17);8066-71. PMID: 2453510

Richterich93: Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. (1993). "Automated multiplex sequencing of the E.coli genome." Data submission to EMBL/GenBank/DDBJ databases on 1993-10.

Saporito88: Saporito SM, Cunningham RP (1988). "Nucleotide sequence of the nfo gene of Escherichia coli K-12." J Bacteriol 170(11);5141-5. PMID: 2460435

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Other References Related to Gene Regulation

Fawcett95: Fawcett WP, Wolf RE (1995). "Genetic definition of the Escherichia coli zwf "soxbox," the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide." J Bacteriol 1995;177(7);1742-50. PMID: 7896696

Jair95: Jair KW, Martin RG, Rosner JL, Fujita N, Ishihama A, Wolf RE (1995). "Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters." J Bacteriol 1995;177(24);7100-4. PMID: 8522515

Jair96: Jair KW, Fawcett WP, Fujita N, Ishihama A, Wolf RE (1996). "Ambidextrous transcriptional activation by SoxS: requirement for the C-terminal domain of the RNA polymerase alpha subunit in a subset of Escherichia coli superoxide-inducible genes." Mol Microbiol 1996;19(2);307-17. PMID: 8825776

Li94b: Li Z, Demple B (1994). "SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA." J Biol Chem 1994;269(28);18371-7. PMID: 8034583

Martin99: Martin RG, Gillette WK, Rhee S, Rosner JL (1999). "Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter." Mol Microbiol 1999;34(3);431-41. PMID: 10564485

Rodionov01: Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB (2001). "Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria." J Mol Microbiol Biotechnol 3(2);319-24. PMID: 11321589

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Mon Aug 31, 2015, biocyc13.